I am using Free2bind software to calculate the binding energy between a motif and the 5'-UTR, but I encountered error: 3' dangle Gs, how can I fix it?

Minh-Nhat Truong-Ha @Minh-Nhat-Truong-Ha

07 October 2020 0 3K Report

I currently want to calculate the binding strength and location between the anti-SD motif and the UTR sequences in E. coli genomes, so I chose to use free2bind based on the article below:Article Predicting Shine–Dalgarno Sequence Locations Exposes Genome ...

However, there are some of my sequences when ran using free_align.pl encountered an error like this:

ERROR: FreeAlign::dangling_3prime()

ERROR: 3' dangle G

C not scored yet...

If anyone have used this application, could you help me with the solution/recommendation to this problem? Thank you very much. the code I used to run is like this: './free_align.pl -l 0 -b 0 seq uccucc > result.txt' , where seq is the input UTR sequence.

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